Mexico's President Felipe Calderon has praised marines for killing the leader of the Zetas drug cartel, Heriberto Lazcano - known as "The Executioner".
The navy said fingerprint tests had confirmed the man killed was Lazcano.
He died in a shootout with marines on Sunday in Coahuila, but his corpse was later stolen by an armed gang from a funeral home in the northern state.
Mr Calderon said the drugs boss was killed while resisting arrest, but did not mention the theft of his body.
Infamous for mass killings, the Zetas control key drug-trafficking routes in north-eastern Mexico.
Lazcano was killed in a gun battle with marines on Sunday in Progreso, some 125km (80 miles) west of the Texan border in Coahuila, the navy said.
It said fingerprints and photographs of the body were taken before it was handed over to local authorities and transported to a funeral parlour - from where it was seized by gunmen and driven away in a hijacked hearse early on Monday morning.
Mr Calderon praised the marines for the operation, and said the navy had made a significant impact on criminal organisations operating in the region.
"With this, Mexico has neutralised, during my government, 25 out of 37 of the most wanted criminals in the country," added the outgoing president.
But the theft of the corpse has undoubtedly taken the gloss off this episode for Mexico's government, says the BBC's Will Grant in Mexico City, as it denies them the ability to parade Lazcano in front of the world's media.
It also throws a shadow of doubt over what happened in a country that thrives on rumour and counter-rumour, especially in relation to its violent drugs war, says our correspondent.
Nevertheless, he adds, Mr Calderon will still be quietly celebrating the fact that Lazcano is no longer a threat in Mexico and that Los Zetas seems to be an organisation in some disarray.
Mr Calderon was speaking on Tuesday during a visit to a new federal prison in the state of Guanajuato.
Navy at forefront
Lazcano was suspected of involvement in hundreds of killings, including that of crusading newspaper editor Francisco Ortiz Franco in 2004.
The US had put up a $5m (£3.1m) reward and Mexico another $2.3m for information leading to the drug boss's capture.
Mexican police believe a recent surge in mass killings has been due to a split within the Zetas cartel.
Lazcano was thought to be the leader of one faction, while the other is led by Miguel Angel Trevino Morales.
In nearly six years of Felipe Calderon's presidency, more than 50,000 people are believed to have died in violence blamed on organised crime.
The navy has been at the forefront of operations against Mexico's drug cartels.